http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.861426
ORIGINAL ARTICLE
Complete mitochondrial genome sequence of the Barbour’s seahorse Hippocampus barbouri Jordan & Richardson, 1908 (Gasterosteiformes: Syngnathidae) Bo Wang1*, Yanhong Zhang2*, Huixian Zhang2, and Qiang Lin2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 12/28/14 For personal use only.
1
Laboratory of Zoology, College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai, Guangdong, China and 2Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China Abstract
Keywords
The complete mitochondrial genome sequence of the Barbour’s seahorse Hippocampus barbouri was first determined in this paper. The total length of H. barbouri mitogenome is 16,526 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of the H. barbouri mitochondrial genome were similar to the typical vertebrates. The overall base composition of H. barbouri is 32.68% A, 29.75% T, 22.91% C and 14.66% G, with an AT content of 62.43%.
Genome composition, Hippocampus barbouri, mitochondrial genome History Received 8 October 2013 Accepted 24 October 2013 Published online 10 January 2014
Table 1. Organization of the mitochondrial genome of H. barbouri.
The Barbour’s seahorse, Hippocampus barbouri Jordan & Richardson, 1908 (Gasterosteiformes: Syngnathidae), is commercially important species in both traditional medicine and aquarium trades (Lourie et al., 2005), and it is shallow-water species generally found in seagrass less than 10 m deep (Lourie et al., 1999). Such habitats tend to be scattered along coastlines, often in sheltered bays that may be separated from each other by unsuitable habitat (Lourie et al., 2005). It has been listed as ‘‘vulnerable’’ on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List (IUCN, 2003) and inclusion on the CITES Appendix II (CITES, 2003). In the present study, we determined the complete mitochondrial genome of the Barbour’s seahorse H. barbouri using a small amount of muscle from the tail of fresh seahorse with the GenBank Accession No. KF712276. All seahorse samples used in this study were with Animal Ethics approval for experimentation granted by the Chinese Academy of Sciences. Primers were designed according to the mitochondrial genome sequence of H. kuda (AP005985) (Kawahara et al., 2008) and H. erectus (KF557652) (Zhang et al., 2013). The complete mitogenome of H. barbouri was 16,526 bp long, and it consisted of 13 protein-coding genes, 22 tRNA genes, 12S rRNA gene, 16S rRNA gene and a putative control region (D-loop) (Table 1). The heavy DNA strand (H-strand) carried most of the genes: 12 protein-coding genes, 2 rRNA and 14 tRNA. ND6 and eight tRNA genes were encoded on the L-strand (Table 1). The structure and composition of H. barbouri mitochondrial genome were similar to the typical vertebrates (Broughton et al., 2001; Noack et al., 1996; Peng et al., 2006). *These authors contributed equally to this work. Correspondence: Qiang Lin, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China. Tel: +86 20 89023161. Fax: +86 20 89022611. E-mail: [email protected]
Position no. Feature tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu (UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COXI tRNASer (UCN) tRNAAsp COXII tRNALys ATPase8 ATPase6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu (CUN) ND5 ND6 tRNAGlu
Codon
Start
Stop
Size (bp)
1 72 1012 1085 2776 2850 3826 3897 3969 4039 5078 5150 5220 5293 5329 5395 5463 7017 7101 7173 7864 7940 8098 8781 9565 9635 9984 10,053 10,343 11,724 11,793 11,863 11,936 13,768 14,290
71 1011 1084 2775 2849 3824 3897 3967 4038 5079 5148 5218 5292 5328 5394 5461 7016 7087 7168 7863 7938 8107 8781 9564 9634 9985 10,052 10,349 11,723 11,792 11,860 11,935 13,771 14,289 14,358
71 940 73 1691 74 975 72 71 70 1041 71 69 73 36 66 67 1554 71 68 691 75 168 684 784 70 351 69 297 1381 69 68 73 1836 522 69
Start
Intergenic Stop nucletides* Strandþ
ATG TAA
ATG TAA
GTG TAA ATG
T– –
ATG TAA ATG TAA ATG T– – ATG TAA ATG TAA ATG T– –
ATG TAA ATG TAA
0 0 0 0 0 1 1 1 0 2 1 1 0 0 0 1 0 13 4 0 1 10 1 0 0 2 0 7 0 0 2 0 4 0 4
H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H L L (continued )
2
B. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Declaration of interest
Table 1. Continued Position no. Feature
Start
Cytb tRNAThr tRNAPro D-loop
14,363 15,504 15,575 15,646
Stop
Codon Size (bp)
Start
15,503 1141 ATG 15,575 72 15,645 71 16,526 881
Intergenic Stop nucletides* Strandþ T– –
0 1 0 0
H H L
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 12/28/14 For personal use only.
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. þ H and L indicate genes transcribed on the heavy and light strands, respectively.
The total base composition of H. barbouri mitochondrial genome was 32.68% A, 29.75% T, 22.91% C and 14.66% G, in the order A4T4C4G, with an AT content of 62.43%. There were 8 regions of gene overlap totaling 28 bp (ranging from 1 to 10 bp) and 10 inter-genic spacer regions totaling 29 bp (ranging from 1 to 13 bp). The total length of the 13 protein-coding genes was 11,425 bp, which represented 69.13% of the entire mitochondrial genome. The longest gene was ND5 (1836 bp), located between tRNALeu (CUN) and ND6, and the shortest was ATPase8 (168 bp), which was between tRNALys and ATPase6. All protein-coding genes stared with the regular initiation codon ATG, except for COXI starting with GTG. TAA, found in nine protein-coding genes (ND1, ND2, ND3, ND4L, ND5, ND6, COXI, ATPase6 and ATPase8), although COXII, ND4 were the typical stop codon. COXII and Cytb ended with Txx (Table 1). The xx was the 50 terminal of the adjacent gene, which presumptively formed a complete stop codon TAA by post-transcriptional polyadenylation (Anderson et al., 1981). Barbour’s seahorse mtDNA contained a small subunit (12S rRNA) and a large subunit (16S rRNA) of rRNA. They were located between tRNAPhe and tRNALeu (UUR), and were separated by tRNAVal. The lengths of the 12S rRNA gene and 16S rRNA gene were 940 and 1691 bp, respectively. The lengths of 22 tRNA genes ranged from 66 to 75 bp; the longest tRNA was tRNALys (75 bp) and the shortest was tRNACys (66 bp). All of the tRNA genes could be folded into the typical cloverleafshaped secondary structure. The D-loop region was located between tRNAPho and tRNAPhe with 881 bp long. The length of putative initiation site for light strand replication (OL) was 36 bp, which was located between tRNAAsn and tRNACys.
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported by the National Natural Science Foundation of China (No. 41176146 and No. 41306148), the National Outstanding Youth Foundation (S2013050014802), the Natural Science Foundation of Guangdong Province of China (S2013040016935), and the Science and Technology Program of Guangdong Province (2011B020307005).
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Broughton RE, Milam JE, Roe BA. (2001). The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11: 1958–67. CITES. (2003). Proposals for amendment of Appendices I and II. Results of the 12th Meeting of the Conference of the Parties 2002. Convention on International Trade in Endangered Species of Wild Fauna and Flora Secretariat, Geneva, Switzerland. Available at: http://www.cites.org/ eng/news/world/cop12_prop_results.pdf (Accessed 20 September 2013). IUCN. (2003). The IUCN Red List of Threatened Species. IUCN (TheWorld Conservation Union) Species Survival Commission, Gland, Switzerland. Available at: http://www.redlist.org (Accessed 20 September 2013). Kawahara R, Miya M, Mabuchi K, Lavoue S, Inoue JG, Satoh TP, Kawaguchi A, Nishida M. (2008). Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol Phylogenet Evol 46:224–36. Lourie SA, Vincent ACJ, Hall HJ. (1999). Seahorse: An identification guide to the world’s species and their conservation. Project Seahorse, London. 214 pp. Lourie SA, Green DM, Vincent AC. (2005). Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus). Mol Ecol 14:1073–94. Noack K, Zardoya R, Meyer A. (1996). The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: Ancient establishment of the consensus vertebrate gene order. Genetics 144:1165–80. Peng ZG, Wang J, He SP. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376: 290–7. Zhang YH, Zhang HX, Lin Q Huang LM. (2013). Complete mitochondrial genome sequence of the lined seahorse Hippocampus erectus Perry, 1810 (Gasterosteiformes: Syngnathidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.840595.
ORIGINAL ARTICLE
Complete mitochondrial genome sequence of the Barbour’s seahorse Hippocampus barbouri Jordan & Richardson, 1908 (Gasterosteiformes: Syngnathidae) Bo Wang1*, Yanhong Zhang2*, Huixian Zhang2, and Qiang Lin2
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 12/28/14 For personal use only.
1
Laboratory of Zoology, College of Engineering and Technology, Beijing Normal University, Zhuhai Campus, Zhuhai, Guangdong, China and 2Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China Abstract
Keywords
The complete mitochondrial genome sequence of the Barbour’s seahorse Hippocampus barbouri was first determined in this paper. The total length of H. barbouri mitogenome is 16,526 bp, which consists of 13 protein-coding genes, 22 tRNA and 2 rRNA genes and 1 control region. The features of the H. barbouri mitochondrial genome were similar to the typical vertebrates. The overall base composition of H. barbouri is 32.68% A, 29.75% T, 22.91% C and 14.66% G, with an AT content of 62.43%.
Genome composition, Hippocampus barbouri, mitochondrial genome History Received 8 October 2013 Accepted 24 October 2013 Published online 10 January 2014
Table 1. Organization of the mitochondrial genome of H. barbouri.
The Barbour’s seahorse, Hippocampus barbouri Jordan & Richardson, 1908 (Gasterosteiformes: Syngnathidae), is commercially important species in both traditional medicine and aquarium trades (Lourie et al., 2005), and it is shallow-water species generally found in seagrass less than 10 m deep (Lourie et al., 1999). Such habitats tend to be scattered along coastlines, often in sheltered bays that may be separated from each other by unsuitable habitat (Lourie et al., 2005). It has been listed as ‘‘vulnerable’’ on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List (IUCN, 2003) and inclusion on the CITES Appendix II (CITES, 2003). In the present study, we determined the complete mitochondrial genome of the Barbour’s seahorse H. barbouri using a small amount of muscle from the tail of fresh seahorse with the GenBank Accession No. KF712276. All seahorse samples used in this study were with Animal Ethics approval for experimentation granted by the Chinese Academy of Sciences. Primers were designed according to the mitochondrial genome sequence of H. kuda (AP005985) (Kawahara et al., 2008) and H. erectus (KF557652) (Zhang et al., 2013). The complete mitogenome of H. barbouri was 16,526 bp long, and it consisted of 13 protein-coding genes, 22 tRNA genes, 12S rRNA gene, 16S rRNA gene and a putative control region (D-loop) (Table 1). The heavy DNA strand (H-strand) carried most of the genes: 12 protein-coding genes, 2 rRNA and 14 tRNA. ND6 and eight tRNA genes were encoded on the L-strand (Table 1). The structure and composition of H. barbouri mitochondrial genome were similar to the typical vertebrates (Broughton et al., 2001; Noack et al., 1996; Peng et al., 2006). *These authors contributed equally to this work. Correspondence: Qiang Lin, Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, China. Tel: +86 20 89023161. Fax: +86 20 89022611. E-mail: [email protected]
Position no. Feature tRNAPhe 12S rRNA tRNAVal 16S rRNA tRNALeu (UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn OL tRNACys tRNATyr COXI tRNASer (UCN) tRNAAsp COXII tRNALys ATPase8 ATPase6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu (CUN) ND5 ND6 tRNAGlu
Codon
Start
Stop
Size (bp)
1 72 1012 1085 2776 2850 3826 3897 3969 4039 5078 5150 5220 5293 5329 5395 5463 7017 7101 7173 7864 7940 8098 8781 9565 9635 9984 10,053 10,343 11,724 11,793 11,863 11,936 13,768 14,290
71 1011 1084 2775 2849 3824 3897 3967 4038 5079 5148 5218 5292 5328 5394 5461 7016 7087 7168 7863 7938 8107 8781 9564 9634 9985 10,052 10,349 11,723 11,792 11,860 11,935 13,771 14,289 14,358
71 940 73 1691 74 975 72 71 70 1041 71 69 73 36 66 67 1554 71 68 691 75 168 684 784 70 351 69 297 1381 69 68 73 1836 522 69
Start
Intergenic Stop nucletides* Strandþ
ATG TAA
ATG TAA
GTG TAA ATG
T– –
ATG TAA ATG TAA ATG T– – ATG TAA ATG TAA ATG T– –
ATG TAA ATG TAA
0 0 0 0 0 1 1 1 0 2 1 1 0 0 0 1 0 13 4 0 1 10 1 0 0 2 0 7 0 0 2 0 4 0 4
H H H H H H H L H H H L L L L L H L H H H H H H H H H H H H H H L L (continued )
2
B. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Declaration of interest
Table 1. Continued Position no. Feature
Start
Cytb tRNAThr tRNAPro D-loop
14,363 15,504 15,575 15,646
Stop
Codon Size (bp)
Start
15,503 1141 ATG 15,575 72 15,645 71 16,526 881
Intergenic Stop nucletides* Strandþ T– –
0 1 0 0
H H L
Mitochondrial DNA Downloaded from informahealthcare.com by University of Guelph on 12/28/14 For personal use only.
*Positive numbers indicate the number of nucleotides found in intergenic spacers between different genes. Negative numbers indicate overlapping nucleotides between adjacent genes. þ H and L indicate genes transcribed on the heavy and light strands, respectively.
The total base composition of H. barbouri mitochondrial genome was 32.68% A, 29.75% T, 22.91% C and 14.66% G, in the order A4T4C4G, with an AT content of 62.43%. There were 8 regions of gene overlap totaling 28 bp (ranging from 1 to 10 bp) and 10 inter-genic spacer regions totaling 29 bp (ranging from 1 to 13 bp). The total length of the 13 protein-coding genes was 11,425 bp, which represented 69.13% of the entire mitochondrial genome. The longest gene was ND5 (1836 bp), located between tRNALeu (CUN) and ND6, and the shortest was ATPase8 (168 bp), which was between tRNALys and ATPase6. All protein-coding genes stared with the regular initiation codon ATG, except for COXI starting with GTG. TAA, found in nine protein-coding genes (ND1, ND2, ND3, ND4L, ND5, ND6, COXI, ATPase6 and ATPase8), although COXII, ND4 were the typical stop codon. COXII and Cytb ended with Txx (Table 1). The xx was the 50 terminal of the adjacent gene, which presumptively formed a complete stop codon TAA by post-transcriptional polyadenylation (Anderson et al., 1981). Barbour’s seahorse mtDNA contained a small subunit (12S rRNA) and a large subunit (16S rRNA) of rRNA. They were located between tRNAPhe and tRNALeu (UUR), and were separated by tRNAVal. The lengths of the 12S rRNA gene and 16S rRNA gene were 940 and 1691 bp, respectively. The lengths of 22 tRNA genes ranged from 66 to 75 bp; the longest tRNA was tRNALys (75 bp) and the shortest was tRNACys (66 bp). All of the tRNA genes could be folded into the typical cloverleafshaped secondary structure. The D-loop region was located between tRNAPho and tRNAPhe with 881 bp long. The length of putative initiation site for light strand replication (OL) was 36 bp, which was located between tRNAAsn and tRNACys.
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. This research was supported by the National Natural Science Foundation of China (No. 41176146 and No. 41306148), the National Outstanding Youth Foundation (S2013050014802), the Natural Science Foundation of Guangdong Province of China (S2013040016935), and the Science and Technology Program of Guangdong Province (2011B020307005).
References Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, et al. (1981). Sequence and organization of the human mitochondrial genome. Nature 290:457–64. Broughton RE, Milam JE, Roe BA. (2001). The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. Genome Res 11: 1958–67. CITES. (2003). Proposals for amendment of Appendices I and II. Results of the 12th Meeting of the Conference of the Parties 2002. Convention on International Trade in Endangered Species of Wild Fauna and Flora Secretariat, Geneva, Switzerland. Available at: http://www.cites.org/ eng/news/world/cop12_prop_results.pdf (Accessed 20 September 2013). IUCN. (2003). The IUCN Red List of Threatened Species. IUCN (TheWorld Conservation Union) Species Survival Commission, Gland, Switzerland. Available at: http://www.redlist.org (Accessed 20 September 2013). Kawahara R, Miya M, Mabuchi K, Lavoue S, Inoue JG, Satoh TP, Kawaguchi A, Nishida M. (2008). Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): A new perspective based on whole mitogenome sequences from 75 higher teleosts. Mol Phylogenet Evol 46:224–36. Lourie SA, Vincent ACJ, Hall HJ. (1999). Seahorse: An identification guide to the world’s species and their conservation. Project Seahorse, London. 214 pp. Lourie SA, Green DM, Vincent AC. (2005). Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus). Mol Ecol 14:1073–94. Noack K, Zardoya R, Meyer A. (1996). The complete mitochondrial DNA sequence of the bichir (Polypterus ornatipinnis), a basal ray-finned fish: Ancient establishment of the consensus vertebrate gene order. Genetics 144:1165–80. Peng ZG, Wang J, He SP. (2006). The complete mitochondrial genome of the helmet catfish Cranoglanis bouderius (Siluriformes: Cranoglanididae) and the phylogeny of otophysan fishes. Gene 376: 290–7. Zhang YH, Zhang HX, Lin Q Huang LM. (2013). Complete mitochondrial genome sequence of the lined seahorse Hippocampus erectus Perry, 1810 (Gasterosteiformes: Syngnathidae). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.840595.
